Screening DNA Methylation in Bodily Fluids for Early Cancer Diagnostics

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The most studied epigenetic abnormality in cancer is gene silencing associated with DNA hypermethylation. Recent studies demonstrate that gene inactivation by promoter hypermethylation can occur at early stages of cancer progression, perhaps even before mutations can be detected. Using DNA methylation as a cancer biomarker shows great promise for early diagnosis, assessments in high risk individuals, and post-therapy monitoring. While a noninvasive test with bodily fluids to detect cancer is seen as a holy grail by clinicians, the ability to detect specific DNA methylation changes in bodily fluids, including blood, sputum or stool represents a greater challenge, due to the small amounts of DNA available in these samples and the limited tumor content of such samples. Therefore, a clinically useful technology that allows for detection of DNA methylation in bodily fluids will have a substantial impact in both cancer diagnosis and management. We propose to develop a new methylation detection platform which integrates improved methods for each of the critical processes involved: DNA isolation, bisulfite treatment, and detection of methylation. All steps will ultimately be integrated and performed on a microfiuidic chip, utilizing superparamagnetic particles as a common carrier for fluidic and molecular manipulations and the quantum dots-mediated fluorescence resonance energy transfer technology (QD-FRET) for biosensing. This approach will facilitate highly efficient sample preparation and sensitive detection of DNA methylation in bodily fluids. In addition, the proposed technology can perform integrated and automatic analysis, minimizing manual labor and time while providing more reproducible results and being useful for a large scale screening. The potential use in pre-cUnical applications will be determined by testing bodily samples from patients with early stage cancers and controls, including serum/plasma, sputum and stool. In addition, the detection of cancer specific methylation in the blood/plasma will be used to monitor therapeutic response in Projects 2, 3 and 4, facihtating development prior to examination of cancer patients.